A manager’s guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance
marine ecosystem/biodiversity monitoring programs. Here we outline five
important steps managers and researchers should consider when developing
eDNA monitoring program: 1) select genes and primers to target focal taxa;
2) assemble or develop comprehensive barcode reference databases; 3) apply
rigorous site occupancy based decontamination pipelines; 4) conduct pilot
studies to define spatial and temporal variance of eDNA; and 5) archive
samples, extracts, and raw sequence data. We demonstrate the importance of
each of these considerations using a case study of eDNA metabarcoding in
the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches
detected 94.1% (16/17) of species observed in paired trawl surveys while
identifying an additional 55 native fishes and provided more comprehensive
biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding
results improved ecological interpretation and confidence in species
detections while providing archived genetic resources for future analyses.
Well designed and validated eDNA metabarcoding approaches are ideally
suited for biomonitoring applications that rely on the detection of
species, including mapping invasive species fronts and endangered species
habitats as well as tracking range shifts in response to climate change.
Incorporating these considerations will enhance the utility and efficacy
of eDNA metabarcoding for routine biomonitoring applications.